August 30, 2014

The Ebola outbreak: That others may live

It is a solemn custom in science to mark the names of collaborators who pass away during the course of an article's publication with a superscript no different than that indicating their academic affiliation. Very rare indeed is the case that five names on a single report should share that mark. Such a report was published in Science this week. It demonstrates the astonishing speed at which genetic sequencing can now be carried out. At the same time, the fact that Ebola claimed five of its authors is testament to the deadliness of the paper's subject.

On June 4th, Stephen Gire, a public health researcher at the Broad Institute in Cambridge, Massachusetts, took delivery of a polystyrene box from Kenema, Sierra Leone. Inside were vials of deactivated biological samples from 78 patients suspected to have Ebola. Mr Gire and a colleague began to tease out the letters of each virus sample's genetic code with some of the most advanced technology yet devised for the task; before long, half of Mr Gire's 30-strong laboratory had volunteered to help.

Then, those sequences of genetic letters were fed into a computer model that looks for hints of mutations where the letters differ. The particular mutations that separate each sample gave hints as to how closely related each was and, because mutations happen naturally at a predictable rate, how long ago they diverged from a common ancestor virus. The networks of transmission from one person to another were laid bare in a laboratory half a world away.

The data suggest that the virus that has now killed more than 1,400 and infected more than 3,000 arose as a distinct strain in 2004. It descended from the 1976 Zaire variant, which usually emerges in central Africa. It may have been lurking in Guinea in the interim, in the "natural reservoir"—presumed to be an animal such as a fruitbat, which can carry the virus without harm.

The outbreaks in Guinea and Sierra Leone, as was suspected, appear to have emerged from a single point of contact with the reservoir, and it seems all of the known cases in Sierra Leone stem from one group of women who attended the funeral of a traditional healer in Guinea in May.

All this insight was gleaned in record time. In all, the genetic sequencing—a quadrupling of the world's genetic knowledge of Ebola—took five days. The computational analysis took four more. Even compared to just a few years ago, that is an extraordinary pace. Mr Gire is now working to accomplish the same wizardry in the places where the outbreaks occur. He runs a programme sponsored by the World Bank to provide the technological tools and the training to scientists in Nigeria and Sierra Leone within the next two years.

Such near-real-time feedback to front-line researchers could head off the transition to a pandemic, helping to spot mutations that change its virulence or its transmission characteristics. It could also help epidemiologists pick up where field studies fall off, honing the understanding of human factors in the spread of disease.

And as the blog post concludes, that understanding has been gained at a very high cost.

Comments

It is a solemn custom in science to mark the names of collaborators who pass away during the course of an article's publication with a superscript no different than that indicating their academic affiliation. Very rare indeed is the case that five names on a single report should share that mark. Such a report was published in Science this week. It demonstrates the astonishing speed at which genetic sequencing can now be carried out. At the same time, the fact that Ebola claimed five of its authors is testament to the deadliness of the paper's subject.

On June 4th, Stephen Gire, a public health researcher at the Broad Institute in Cambridge, Massachusetts, took delivery of a polystyrene box from Kenema, Sierra Leone. Inside were vials of deactivated biological samples from 78 patients suspected to have Ebola. Mr Gire and a colleague began to tease out the letters of each virus sample's genetic code with some of the most advanced technology yet devised for the task; before long, half of Mr Gire's 30-strong laboratory had volunteered to help.

Then, those sequences of genetic letters were fed into a computer model that looks for hints of mutations where the letters differ. The particular mutations that separate each sample gave hints as to how closely related each was and, because mutations happen naturally at a predictable rate, how long ago they diverged from a common ancestor virus. The networks of transmission from one person to another were laid bare in a laboratory half a world away.

The data suggest that the virus that has now killed more than 1,400 and infected more than 3,000 arose as a distinct strain in 2004. It descended from the 1976 Zaire variant, which usually emerges in central Africa. It may have been lurking in Guinea in the interim, in the "natural reservoir"—presumed to be an animal such as a fruitbat, which can carry the virus without harm.

The outbreaks in Guinea and Sierra Leone, as was suspected, appear to have emerged from a single point of contact with the reservoir, and it seems all of the known cases in Sierra Leone stem from one group of women who attended the funeral of a traditional healer in Guinea in May.

All this insight was gleaned in record time. In all, the genetic sequencing—a quadrupling of the world's genetic knowledge of Ebola—took five days. The computational analysis took four more. Even compared to just a few years ago, that is an extraordinary pace. Mr Gire is now working to accomplish the same wizardry in the places where the outbreaks occur. He runs a programme sponsored by the World Bank to provide the technological tools and the training to scientists in Nigeria and Sierra Leone within the next two years.

Such near-real-time feedback to front-line researchers could head off the transition to a pandemic, helping to spot mutations that change its virulence or its transmission characteristics. It could also help epidemiologists pick up where field studies fall off, honing the understanding of human factors in the spread of disease.

And as the blog post concludes, that understanding has been gained at a very high cost.